Dataset formats

The input datasets are in gd_snp, gd_genotype, text, and gd_indivs formats. The output dataset is in text format.

What it does

The user provides a Galaxy SNP table (gd_snp or gd_genotype format) that includes the founders of a pedigree, as well as two sets of individuals. The pedigree is specified by a text file with one row per individual, containing (1) the individual's name, (2) the name of one of the individual's parents, which must have occurred at the start of a previous line, and (3) the name of the individual's other parent, which occurred at the start of a previous line. For a pedigree founder, both parent names are replaced by "-". The founders are specified by a table in gd_indivs format, e.g., as produced by "Specify individuals" tool. Every founder must have genotypes supplied in the SNP table, and both parents need to be given as "-" in the pedigree. Conversely, every pedigree individual whose parents are "-" must be named as a founder.

The user also provides two files that specify a set of names of individuals. The first word on each line names an individual (one line per individual); any subsequent information on a line is ignored. The name of each individual must appear at the start of a line in the pedigree.

For each pair of individuals, one from each specified set, the program computes the expected heterozygosity of any offspring of the pair, i.e., the probability that the offspring has distinct nucleotides at a randomly chosen autosomal SNP. A SNP is ignorned if one or both potential parents have an ancestor with undefined genotype (designated as -1 in the SNP table).